package com.example.phobosMine;

import java.util.ArrayList;

import com.biomatters.geneious.publicapi.plugin.Options;
import com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption;

public class PhobosOptions extends Options {
	public PhobosOptions(){
		codeLocationOptions();
	}
	
	private FileSelectionOption codeLocation;
	
	private void codeLocationOptions(){
		codeLocation = addFileSelectionOption("EXE","The location of the phobos binary","");
		codeLocation.setRestoreDefaultApplies(false);
	}
	
	public String[] getCommand(String tempFile){
		ArrayList<String> commandList = new ArrayList<String>();
		
		commandList.add(codeLocation.getValue());
		commandList.add(tempFile);
		commandList.add("--outputFormat 0");
		
		return commandList.toArray(new String[commandList.size()]);
	}
}
